| reverseSeq {Biostrings} | R Documentation |
WARNING: The functions described in this man page have been deprecated
in favor of reverse,XString-method and reverseComplement.
Functions to obtain the reverse and reverse complement of a sequence
reverseSeq(seq) revcompDNA(seq) revcompRNA(seq)
seq |
Character vector. For revcompRNA and
revcompDNA the sequence should consist of appropriate letter
codes: [ACGUN] and ACGTN, respectively. |
The function reverses the order of the constituent character strings of its argument.
A character vector of the same length as seq.
R. Gentleman, W. Huber, S. Falcon
alphabetFrequency, reverseComplement
w <- c("hey there", "you silly fool")
if (interactive()) {
reverseSeq(w) # deprecated (inefficient on large vectors)
}
reverse(BStringSet(w)) # more efficient
w <- "able was I ere I saw Elba"
if (interactive()) {
reverseSeq(w) # deprecated (inefficient on large vectors)
}
reverse(BStringSet(w)) # more efficient
rna1 <- "UGCA"
if (interactive()) {
revcompRNA(rna1) # deprecated (inefficient on large vectors)
}
reverseComplement(RNAString(rna1)) # more efficient
dna1 <- "TGCA"
if (interactive()) {
revcompDNA(dna1) # deprecated (inefficient on large vectors)
}
reverseComplement(DNAString(dna1)) # more efficient
## Comparing efficiencies:
if (interactive()) {
library(hgu95av2probe)
system.time(y1 <- reverseSeq(hgu95av2probe$sequence))
x <- DNAStringSet(hgu95av2probe$sequence)
system.time(y2 <- reverse(x))
system.time(y3 <- revcompDNA(hgu95av2probe$sequence))
system.time(y4 <- reverseComplement(x))
}